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docs update
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@Yunuuuu
Yunuuuu committed Dec 15, 2024
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6 changes: 2 additions & 4 deletions README.Rmd
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Expand Up @@ -98,8 +98,6 @@ remotes::install_github("Yunuuuu/ggalign")
| **Dendrogram Position** | Anywhere | Heatmap only | Anywhere | Heatmap only |
| **3D Heatmap** | Yes | Yes | No | No |
| **Oncoplot** | Yes | Yes | Yes | No |
| **Fully Compatible with ggplot2\*** | Yes | No | No | No |
| **Ease of Use** | Easy for ggplot2 users | Easy for for grid user\* | Easy for python user | Easy |
| **Fully Compatible with ggplot2** | Yes | No | No | No |
| **Ease of Use** | Easy for ggplot2 users | Easy for for grid user | Easy for python user | Easy |
| **Interactive** | No | Yes | No | No |
- `Fully Compatible with ggplot2*`: It can be considered a benefit, as the ggplot2 ecosystem is highly enriched.
- `Easy for for grid user*`: the direct population using grid should be smaller than ggplot2
59 changes: 26 additions & 33 deletions README.md
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Expand Up @@ -68,36 +68,29 @@ remotes::install_github("Yunuuuu/ggalign")

## Compare with other similar tools

| | `ggalign` | `ComplexHeatmap` | `marsilea` | `ggheatmap` |
|-------------------------------------|-----------------------------------------------------|------------------------------------------------------|--------------------------|------------------------------------------------------|
| **Language** | R | R | Python | R |
| **User Interface** | Declarative | Functional | Declarative | Functional |
| **Plot System** | ggplot2 (Advanced plot system built on grid system) | grid | seaborn | ggplot2 |
| **Focus** | Composable Visualization | Heatmap | Composable Visualization | Heatmap |
| **Heatmap Layout** | Yes | Yes | Yes | Yes |
| **Marginal Layout** | Yes | No | Yes | No |
| **Stack Layout** | Yes | Yes | Yes | No |
| **Cross Layout** | Yes | No | No | No |
| **Group or Reorder Heatmap** | Yes | Yes | Yes | Yes |
| **Group or Reorder Stack Only** | Yes | No | Yes | No |
| **Separate Group into Slices** | Yes | Yes | Yes | No |
| **Data input** | Various, and can be easily extended | fixed | fixed | fixed |
| **Visualization Type** | Wide variety, provided by ggplot2 | Many, but limited | Many, but limited | Limited |
| **Customization** | Extensive | Limited | Extensive | Limited |
| **Legends Creation** | Automatic | Limited automatic, requires manual add | Manual | Automatic |
| **Legends Position** | Anywhere, can be controlled for a single plot | Four sides, can only be placed on one side at a time | ? | Four sides, can only be placed on one side at a time |
| **Advanced Statistical Plots** | Yes, with ggplot2 extension | No | No | No |
| **Scientific Color Palettes** | Many | Limited | Limited | Many |
| **Tanglegram** | Yes | No | Yes | No |
| **Dendrogram Position** | Anywhere | Heatmap only | Anywhere | Heatmap only |
| **3D Heatmap** | Yes | Yes | No | No |
| **Oncoplot** | Yes | Yes | Yes | No |
| **Fully Compatible with ggplot2\*** | Yes | No | No | No |
| **Interoperability with Python** | Limited | Limited | Excellent | Limited |
| **Ease of Use** | Easy for ggplot2 users | Easy for for grid user\* | Easy for python user | Easy |
| **Interactive** | No | Yes | No | No |

- `Fully Compatible with ggplot2*`: It can be considered a benefit, as
the ggplot2 ecosystem is highly enriched.
- `Easy for for grid user*`: the direct population using grid should be
smaller than ggplot2
| | `ggalign` | `ComplexHeatmap` | `marsilea` | `ggheatmap` |
|-----------------------------------|-----------------------------------------------------|------------------------------------------------------|--------------------------|------------------------------------------------------|
| **Language** | R | R | Python | R |
| **User Interface** | Declarative | Functional | Declarative | Functional |
| **Plot System** | ggplot2 (Advanced plot system built on grid system) | grid | seaborn | ggplot2 |
| **Focus** | Composable Visualization | Heatmap | Composable Visualization | Heatmap |
| **Heatmap Layout** | Yes | Yes | Yes | Yes |
| **Marginal Layout** | Yes | No | Yes | No |
| **Stack Layout** | Yes | Yes | Yes | No |
| **Cross Layout** | Yes | No | No | No |
| **Group or Reorder Heatmap** | Yes | Yes | Yes | Yes |
| **Group or Reorder Stack Only** | Yes | No | Yes | No |
| **Separate Group into Slices** | Yes | Yes | Yes | No |
| **Data input** | Various, and can be easily extended | fixed | fixed | fixed |
| **Visualization Type** | Wide variety, provided by ggplot2 | Many, but limited | Many, but limited | Limited |
| **Customization** | Extensive | Limited | Extensive | Limited |
| **Legends Creation** | Automatic | Limited automatic, requires manual add | Manual | Automatic |
| **Legends Position** | Anywhere, can be controlled for a single plot | Four sides, can only be placed on one side at a time | ? | Four sides, can only be placed on one side at a time |
| **Scientific Color Palettes** | Many | Limited | Limited | Many |
| **Tanglegram** | Yes | No | Yes | No |
| **Dendrogram Position** | Anywhere | Heatmap only | Anywhere | Heatmap only |
| **3D Heatmap** | Yes | Yes | No | No |
| **Oncoplot** | Yes | Yes | Yes | No |
| **Fully Compatible with ggplot2** | Yes | No | No | No |
| **Ease of Use** | Easy for ggplot2 users | Easy for for grid user | Easy for python user | Easy |
| **Interactive** | No | Yes | No | No |

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